Pharmaceutical product pipelines and FDA approval rates have weakened dramatically over the past decade. In addition, with recently accelerating discovery of new diagnostic analytes, biomarkers and targets of clinical and industrial interest, there is a growing need for new analytical and clinical reagents and molecular probes. To aid in the discovery of new drug candidate, diagnostic reagents and industrially useful target-binding ligands, the bead-based screening technology described by Drs. Guthold and Macosko (PCT Patent Application WO 2010/091144, published Aug. 12, 2010) was developed. One limitation of the technology described therein is the need for a “pick-up” step (e.g., atomic-force microscopy or micropipette-based bead pick-up) in combination with subsequent sequencing steps, for identification of candidate compounds. While this limitation can potentially be addressed through automation and microminiaturization, there is a need for new, more rapid and cost-effective compound discovery systems and methods to screen, select and identify new and useful ligands, probes and effector molecules.